bio 1.0.0 → 1.1.0

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb

@@ -0,0 +1,100 @@
+#
+# test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_aligned_strands.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/double_stranded/aligned_strands'
+require 'bio/util/restriction_enzyme/double_stranded'
+
+module Bio #:nodoc:
+
+class TestDoubleStrandedAlignedStrands < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
+    @s = Bio::Sequence::NA
+
+    @ds = Bio::RestrictionEnzyme::DoubleStranded
+
+    @s_1 = @s.new('gattaca')
+    @s_2 = @s_1.forward_complement
+
+    @s_3 = @s.new('tttttttnnn')
+    @s_4 = @s.new('nnnaaaaaaa')
+
+    @ds_1 = @ds.new('nnnn^ngattacann^nn^n')
+
+    @obj_1 = @t.align(@s_1, @s_2)
+    @obj_2 = @t.align(@s_1, @s_3)
+    @obj_3 = @t.align(@s_1, @s_4)
+    @obj_4 = @t.align(@s_3, @s_4)
+
+    @obj_5 = @t.align(@ds_1.primary, @ds_1.complement)
+
+    @obj_8 = @t.align_with_cuts(@ds_1.primary, @ds_1.complement, @ds_1.primary.cut_locations, @ds_1.complement.cut_locations)
+
+    @obj_6 = @t.align_with_cuts(@s_1, @s_2, [1,2], [3,4])
+    @obj_7 = @t.align_with_cuts(@s_3, @s_4, [1,2], [3,4])
+
+  end
+
+  def test_ds
+    assert_equal('nngattacannnnn', @ds_1.primary)
+    assert_equal('nnnnnctaatgtnn', @ds_1.complement)
+    assert_equal(    'n^ngattacann^nn^n', @ds_1.primary.with_cut_symbols)
+    assert_equal('n^nn^nnctaatgtn^n'    , @ds_1.complement.with_cut_symbols)
+
+    assert_equal([0, 10, 12], @ds_1.primary.cut_locations)
+    assert_equal([0, 2, 12], @ds_1.complement.cut_locations)
+  end
+
+  def test_align
+    assert_equal('gattaca', @obj_1.primary)
+    assert_equal('ctaatgt', @obj_1.complement)
+
+    assert_equal('gattacannn', @obj_2.primary)
+    assert_equal('tttttttnnn', @obj_2.complement)
+
+    assert_equal('nnngattaca', @obj_3.primary)
+    assert_equal('nnnaaaaaaa', @obj_3.complement)
+
+    assert_equal('nnntttttttnnn', @obj_4.primary)
+    assert_equal('nnnaaaaaaannn', @obj_4.complement)
+
+    assert_equal('nnnnngattacannnnn', @obj_5.primary)
+    assert_equal('nnnnnctaatgtnnnnn', @obj_5.complement)
+  end
+
+  def test_align_with_cuts
+    assert_equal('g a^t^t a c a', @obj_6.primary)
+    assert_equal('c t a a^t^g t', @obj_6.complement)
+
+    # Looks incorrect at first, but this is deliberate.
+    # The correct cuts need to be supplied by the user.
+    assert_equal('n n n t t^t^t t t t n n n', @obj_7.primary)
+    assert_equal('n n n a^a^a a a a a n n n', @obj_7.complement)
+
+    assert_equal('n n n n^n g a t t a c a n n^n n^n', @obj_8.primary)
+    assert_equal('n^n n^n n c t a a t g t n^n n n n', @obj_8.complement)
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new('arg', 'agg') }
+    assert_raise(ArgumentError) { @t.new(@s.new('arg'), 'agg') }
+    assert_raise(ArgumentError) { @t.new('arg', @s.new('agg')) }
+    assert_raise(ArgumentError) { @t.new(@s.new('argg'), @s.new('agg')) }
+  end
+
+end
+
+end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb

@@ -0,0 +1,75 @@
+#
+# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_cut_location_pair.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair'
+
+module Bio #:nodoc:
+
+class TestDoubleStrandedCutLocationPair < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
+
+    @obj_1 = @t.new([3,5])
+    @obj_2 = @t.new(3, 5)
+    @obj_3 = @t.new((3..5))
+    @obj_4 = @t.new(0..5)
+    @obj_5 = @t.new(3)
+    @obj_6 = @t.new(nil,3)
+    @obj_7 = @t.new(3,nil)
+  end
+
+  def test_contents
+    assert_equal([3,5], @obj_1)
+    assert_equal([3,5], @obj_2)
+    assert_equal([3,5], @obj_3)
+    assert_equal([0,5], @obj_4)
+    assert_equal([3,nil], @obj_5)
+    assert_equal([nil,3], @obj_6)
+    assert_equal([3,nil], @obj_7)
+  end
+
+  def test_primary
+    assert_equal(3, @obj_1.primary)
+    assert_equal(3, @obj_2.primary)
+    assert_equal(3, @obj_3.primary)
+    assert_equal(0, @obj_4.primary)
+    assert_equal(3, @obj_5.primary)
+    assert_equal(nil, @obj_6.primary)
+    assert_equal(3, @obj_7.primary)
+  end
+
+  def test_complement
+    assert_equal(5, @obj_1.complement)
+    assert_equal(5, @obj_2.complement)
+    assert_equal(5, @obj_3.complement)
+    assert_equal(5, @obj_4.complement)
+    assert_equal(nil, @obj_5.complement)
+    assert_equal(3, @obj_6.complement)
+    assert_equal(nil, @obj_7.complement)
+  end
+
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new([3,5,6]) }
+    assert_raise(ArgumentError) { @t.new(3,-1) }
+    assert_raise(ArgumentError) { @t.new(-3,1) }
+    assert_raise(ArgumentError) { @t.new(nil,nil) }
+    assert_raise(ArgumentError) { @t.new('3',5) }
+  end
+
+end
+
+end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb

@@ -0,0 +1,73 @@
+#
+# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_cut_location_pair_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation'
+
+module Bio #:nodoc:
+
+class TestDoubleStrandedCutLocationPairInEnzymeNotation < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
+
+    @obj_1 = @t.new([3,5])
+    @obj_2 = @t.new(3, 5)
+    @obj_3 = @t.new((3..5))
+    @obj_4 = @t.new(-3..5)
+    @obj_5 = @t.new(3)
+    @obj_6 = @t.new(nil,3)
+    @obj_7 = @t.new(3,nil)
+  end
+
+  def test_contents
+    assert_equal([3,5], @obj_1)
+    assert_equal([3,5], @obj_2)
+    assert_equal([3,5], @obj_3)
+    assert_equal([-3,5], @obj_4)
+    assert_equal([3,nil], @obj_5)
+    assert_equal([nil,3], @obj_6)
+    assert_equal([3,nil], @obj_7)
+  end
+
+  def test_primary
+    assert_equal(3, @obj_1.primary)
+    assert_equal(3, @obj_2.primary)
+    assert_equal(3, @obj_3.primary)
+    assert_equal(-3, @obj_4.primary)
+    assert_equal(3, @obj_5.primary)
+    assert_equal(nil, @obj_6.primary)
+    assert_equal(3, @obj_7.primary)
+  end
+
+  def test_complement
+    assert_equal(5, @obj_1.complement)
+    assert_equal(5, @obj_2.complement)
+    assert_equal(5, @obj_3.complement)
+    assert_equal(5, @obj_4.complement)
+    assert_equal(nil, @obj_5.complement)
+    assert_equal(3, @obj_6.complement)
+    assert_equal(nil, @obj_7.complement)
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new([3,5,6]) }
+    assert_raise(ArgumentError) { @t.new(0,1) }
+    assert_raise(ArgumentError) { @t.new(0,0) }
+    assert_raise(ArgumentError) { @t.new('3',5) }
+  end
+
+end
+
+end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb

@@ -0,0 +1,53 @@
+#
+# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocations
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_cut_locations.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/double_stranded/cut_locations'
+
+module Bio #:nodoc:
+
+class TestDoubleStrandedCutLocations < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
+    @tt = Bio::RestrictionEnzyme::DoubleStranded::CutLocations
+
+
+    @obj_1 = @t.new([3,5])
+    @obj_2 = @t.new(3, 5)
+    @obj_3 = @t.new((3..5))
+    @obj_4 = @t.new(3..5)
+    @obj_5 = @t.new(3)
+    @obj_6 = @t.new(nil,3)
+    @obj_7 = @t.new(3,nil)
+
+    @locations = @tt.new(@obj_1, @obj_2, @obj_3, @obj_4, @obj_5, @obj_6, @obj_7)
+  end
+
+  def test_contents
+    assert_equal([3,5], @locations[0])
+    assert_equal([3,nil], @locations[-1])
+  end
+
+  def test_primary
+    assert_equal([3, 3, 3, 3, 3, nil, 3], @locations.primary)
+  end
+
+  def test_complement
+    assert_equal([5, 5, 5, 5, nil, 3, nil], @locations.complement)
+  end
+
+end
+
+end

data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb

@@ -0,0 +1,104 @@
+#
+# test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_cut_locations_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation'
+
+module Bio #:nodoc:
+
+class TestDoubleStrandedCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
+    @tt = Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
+
+    @obj_1 = @t.new([3,5])
+    @obj_2 = @t.new(3, 5)
+    @obj_3 = @t.new((3..5))
+    @obj_4 = @t.new(-3..5)
+    @obj_5 = @t.new(3)
+    @obj_6 = @t.new(nil,3)
+    @obj_7 = @t.new(3,nil)
+    @obj_8 = @t.new(-8, -7)
+
+    @locations = @tt.new(@obj_1, @obj_2, @obj_3, @obj_4, @obj_5, @obj_6, @obj_7, @obj_8)
+    @loc_2 = @tt.new(@t.new(-2,-2), @t.new(1,1))
+    @loc_3 = @tt.new(@t.new(1,2))
+  end
+
+  def test_contents
+    assert_equal([3,5], @locations[0])
+    assert_equal([3,nil], @locations[-2])
+  end
+
+  def test_primary
+    assert_equal([3, 3, 3, -3, 3, nil, 3, -8], @locations.primary)
+  end
+
+  def test_complement
+    assert_equal([5, 5, 5, 5, nil, 3, nil, -7], @locations.complement)
+  end
+
+  def test_primary_to_array_index
+    assert_equal([10, 10, 10, 5, 10, nil, 10, 0], @locations.primary_to_array_index)
+    assert_equal([0,2], @loc_2.primary_to_array_index)
+    assert_equal([0], @loc_3.primary_to_array_index)
+  end
+
+  def test_primary_to_array_index_class
+    assert_equal(Array, @locations.primary_to_array_index.class)
+    assert_equal(Array, @loc_2.primary_to_array_index.class)
+  end
+
+  def test_complement_to_array_index
+    assert_equal([12, 12, 12, 12, nil, 10, nil, 1], @locations.complement_to_array_index)
+    assert_equal([0,2], @loc_2.complement_to_array_index)
+    assert_equal([1], @loc_3.complement_to_array_index)
+  end
+
+  def test_complement_to_array_index_class
+    assert_equal(Array, @locations.complement_to_array_index.class)
+    assert_equal(Array, @loc_2.complement_to_array_index.class)
+  end
+
+  def test_to_array_index
+    assert_equal(
+      [
+        [10, 12],
+        [10, 12],
+        [10, 12],
+        [5, 12],
+        [10, nil],
+        [nil, 10],
+        [10, nil],
+        [0, 1]
+      ], @locations.to_array_index)
+
+    assert_equal(
+      [
+        [0, 0],
+        [2, 2],
+      ], @loc_2.to_array_index)
+
+    assert_equal([[0,1]], @loc_3.to_array_index)
+  end
+
+  def test_to_array_index_class
+    assert_equal(Bio::RestrictionEnzyme::DoubleStranded::CutLocations, @locations.to_array_index.class)
+    assert_equal(Bio::RestrictionEnzyme::DoubleStranded::CutLocations, @loc_2.to_array_index.class)
+  end
+
+end
+
+end

data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb

@@ -0,0 +1,83 @@
+#
+# test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb - Unit test for Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
+#
+# Author::    Trevor Wennblom  <mailto:trevor@corevx.com>
+# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
+# License::   The Ruby License
+#
+#  $Id: test_cut_locations_in_enzyme_notation.rb,v 1.3 2007/04/05 23:35:44 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 6, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation'
+
+module Bio #:nodoc:
+
+class TestSingleStrandCutLocationsInEnzymeNotation < Test::Unit::TestCase #:nodoc:
+
+  def setup
+    @t = Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
+    @obj_1 = @t.new([-2,1,3])
+    @obj_2 = @t.new(-2,1,3)
+    @obj_3 = @t.new(7,1,3)
+
+    @obj_4 = @t.new(-7,-8,-2,1,3)
+  end
+
+  def test_max
+    assert_equal(3, @obj_1.max)
+    assert_equal(3, @obj_2.max)
+    assert_equal(7, @obj_3.max)
+  end
+
+  def test_min
+    assert_equal(-2, @obj_1.min)
+    assert_equal(-2, @obj_2.min)
+    assert_equal(1, @obj_3.min)
+  end
+
+  def test_to_array_index
+    assert_equal([0,2,4], @obj_1.to_array_index)
+    assert_equal([0,2,4], @obj_2.to_array_index)
+    assert_equal([0,2,6], @obj_3.to_array_index)
+
+    assert_equal([0, 1, 6, 8, 10], @obj_4.to_array_index)
+  end
+
+  def test_initialize_with_pattern
+    @obj_5 = @t.new('n^ng^arraxt^n')
+    @obj_6 = @t.new('g^arraxt^n')
+    @obj_7 = @t.new('nnn^nn^nga^rraxt^nn')
+    @obj_8 = @t.new('^g^arraxt^n')
+
+    assert_equal([-2,1,7], @obj_5)
+    assert_equal([0,2,8], @obj_5.to_array_index)
+
+    assert_equal([1,7], @obj_6)
+    assert_equal([0,6], @obj_6.to_array_index)
+
+    assert_equal([-4, -2, 2, 7], @obj_7)
+    assert_equal([0, 2, 5, 10], @obj_7.to_array_index)
+    
+    assert_equal([-1,1,7], @obj_8)
+    assert_equal([0,1,7], @obj_8.to_array_index)
+  end
+
+  def test_argument_error
+    assert_raise(ArgumentError) { @t.new([0,1,2]) }
+    assert_raise(ArgumentError) { @t.new(0,1,2,0) }
+
+    assert_raise(ArgumentError) { @t.new([nil,1,2]) }
+    assert_raise(ArgumentError) { @t.new(nil,1,2,nil) }
+
+    assert_raise(ArgumentError) { @t.new([1,1,2]) }
+    assert_raise(ArgumentError) { @t.new(1,1,2,2) }
+  end
+
+end
+
+end